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DEBrowser: interactive differential expression analysis and visualization tool for count data.

Alper Kucukural1,2, Onur Yukselen3, Deniz M Ozata4

  • 1Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA. alper.kucukural@umassmed.edu.

BMC Genomics
|January 7, 2019
PubMed
Summary
This summary is machine-generated.

DEBrowser is a new R bioconductor project that offers an interactive, web-based platform for analyzing sequencing count data. This tool simplifies complex differential analyses, making them accessible without programming skills.

Keywords:
Data visualizationDifferential expressionInteractive data analysis

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing technologies generate vast amounts of data for studying cellular activities.
  • Analysis of sequencing data, such as RNA-Seq and ChIP-Seq, involves processing count tables for differential analysis.
  • Complex analysis pipelines often require programming skills, posing a challenge for many researchers.

Purpose of the Study:

  • To develop an intuitive, interactive platform for visualizing and analyzing sequencing count data.
  • To enable researchers without programming experience to perform differential analyses.
  • To provide tools for assessing and correcting technical variations in sequencing data.

Main Methods:

  • Development of DEBrowser as an R bioconductor project.
  • Implementation of a web-based graphical user interface using R's Shiny infrastructure.
  • Integration of interactive visualization tools for exploring and subsetting data.

Main Results:

  • DEBrowser provides interactive visualization of all differential analysis steps.
  • Users can explore data through various graph types and re-plot subsets.
  • The platform facilitates the identification and correction of technical variations like batch effects and sequencing depth.

Conclusions:

  • DEBrowser is a flexible and intuitive web-based platform.
  • It enables iterative and interactive analysis of count data.
  • No programming knowledge is required to use DEBrowser.